docs: def cmd_ok(cmd):
      """Returns True if cmd can be run.
      """ 
      try:
          sp.check_call(cmd, stderr=sp.PIPE, stdout=sp.PIPE)
      except sp.CalledProcessError:
          # bwa gives return code of 1 with no argument
          pass
      except:
          sys.stderr.write("{} not found, skipping\n".format(cmd))
          return False
      return True